This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to tag debian/2.4.0+dfsg-4 in repository bamtools.
commit 35ac2060e9d33f4a3137126c281f3b055de08d6b Author: Michael R. Crusoe <[email protected]> Date: Sat Mar 5 05:56:22 2016 -0800 Spring cleaning priority->extra; standards version bump Update my email address & tweak Vcs-Git URL split out dev -doc, fix typo, forwad patches quiet some doxygen warnings, add gcc-6 compat, include $devlibs, fixed spelling error in our changelog --- debian/changelog | 19 ++++++- debian/clean | 2 +- debian/control | 26 +++++++-- debian/libbamtools-dev.install | 1 - ...tools-dev.doc-base => libbamtools-doc.doc-base} | 0 ...amtools-dev.install => libbamtools-doc.install} | 1 - debian/libbamtools2.4.0.lintian-overrides | 1 + .../patches/0002-support-out-of-source-build.patch | 2 +- ...bamtools-to-lib.-Installing-libraries-to-.patch | 2 +- .../0006-Fix-Doxyfile-input-source-path.patch | 2 +- debian/patches/0007-Big_Endian.patch | 4 +- debian/patches/doxygen-tweak | 66 ++++++++++++++++++++++ debian/patches/gcc-6_compat | 20 +++++++ .../patches/non-deprecated-jsoncpp-function-names | 15 +++++ debian/patches/series | 4 ++ debian/patches/spelling | 15 +++++ debian/rules | 21 ++++--- 17 files changed, 181 insertions(+), 20 deletions(-) diff --git a/debian/changelog b/debian/changelog index 41c1cc4..343c1a5 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,23 @@ +bamtools (2.4.0+dfsg-4) UNRELEASED; urgency=medium + + * Lower priority to 'extra' due to dependency on libjsoncpp1 + * Split out -doc package for library documentation & enable standalone -arch + and -indep building + * Fix spelling error from upstream + * Update Standards-Version + * Update my email address + * Fix Vcs-Git URL + * Quiet some Doxygen warnings + * Add gcc-6 compat + * Include ${devlibs} for -dev package + * Forwarded many patches upstream + * Remove the html docs directory during d/rules clean + + -- Michael R. Crusoe <[email protected]> Sat, 05 Mar 2016 05:54:38 -0800 + bamtools (2.4.0+dfsg-3) unstable; urgency=medium - * allow to read bam files on big endian systems (Closes: #807979) + * allows one to read bam files on big endian systems (Closes: #807979) * added sam_spec_example.sam and sam_spec_example.bam files * activated cmake testing framework abd added simple tests diff --git a/debian/clean b/debian/clean index 3675a60..991c2c6 100644 --- a/debian/clean +++ b/debian/clean @@ -2,4 +2,4 @@ bin/* lib/* include/* src/toolkit/bamtools_version.h - +html/ diff --git a/debian/control b/debian/control index 5d51cb8..226bb57 100644 --- a/debian/control +++ b/debian/control @@ -1,11 +1,11 @@ Source: bamtools Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Michael R. Crusoe <[email protected]>, +Uploaders: Michael R. Crusoe <[email protected]>, Andreas Tille <[email protected]>, Kevin Murray <[email protected]>, Dominique Belhachemi <[email protected]> Section: science -Priority: optional +Priority: extra Build-Depends: debhelper (>= 9.0.0), d-shlibs (>= 0.56), cmake, @@ -13,9 +13,9 @@ Build-Depends: debhelper (>= 9.0.0), libjsoncpp-dev, help2man, doxygen -Standards-Version: 3.9.6 +Standards-Version: 3.9.7 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bamtools.git -Vcs-Git: https://anonscm.debian.org/cgit/debian-med/bamtools.git +Vcs-Git: https://anonscm.debian.org/git/debian-med/bamtools.git Homepage: https://github.com/pezmaster31/bamtools/wiki Package: bamtools @@ -55,7 +55,9 @@ Package: libbamtools-dev Architecture: any Section: libdevel Depends: libbamtools2.4.0 (= ${binary:Version}), + ${devlibs:Depends}, ${misc:Depends} +Suggests: libbamtools-doc (= ${binary:Version}) Description: C++ API for manipulating BAM (genome alignment) files BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current @@ -84,3 +86,19 @@ Description: dynamic library for manipulating BAM (genome alignment) files command-line toolkit. . This is the runtime library. + +Package: libbamtools-doc +Architecture: all +Section: doc +Depends: ${misc:Depends} +Description: docs for dynamic library for manipulating BAM (genome alignment) files + BamTools facilitates research analysis and data management using BAM + files. It copes with the enormous amount of data produced by current + sequencing technologies that is typically stored in compressed, binary + formats that are not easily handled by the text-based parsers commonly + used in bioinformatics research. + . + BamTools provides both a C++ API for BAM file support as well as a + command-line toolkit. + . + This is the documentation for the library. diff --git a/debian/libbamtools-dev.install b/debian/libbamtools-dev.install index 5f4df6f..7687141 100644 --- a/debian/libbamtools-dev.install +++ b/debian/libbamtools-dev.install @@ -1,2 +1 @@ debian/cmake usr/share -html usr/share/doc/libbamtools-dev diff --git a/debian/libbamtools-dev.doc-base b/debian/libbamtools-doc.doc-base similarity index 100% rename from debian/libbamtools-dev.doc-base rename to debian/libbamtools-doc.doc-base diff --git a/debian/libbamtools-dev.install b/debian/libbamtools-doc.install similarity index 61% copy from debian/libbamtools-dev.install copy to debian/libbamtools-doc.install index 5f4df6f..c49fe91 100644 --- a/debian/libbamtools-dev.install +++ b/debian/libbamtools-doc.install @@ -1,2 +1 @@ -debian/cmake usr/share html usr/share/doc/libbamtools-dev diff --git a/debian/libbamtools2.4.0.lintian-overrides b/debian/libbamtools2.4.0.lintian-overrides index a91ee70..536b82d 100644 --- a/debian/libbamtools2.4.0.lintian-overrides +++ b/debian/libbamtools2.4.0.lintian-overrides @@ -1 +1,2 @@ libbamtools2.4.0: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libbamtools.so.2.4.0 ment meant +libbamtools2.4.0: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libbamtools.so.2.4.0 unknow unknown diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch index e5d1eb0..ae8f236 100644 --- a/debian/patches/0002-support-out-of-source-build.patch +++ b/debian/patches/0002-support-out-of-source-build.patch @@ -1,7 +1,7 @@ From: Dominique Belhachemi <[email protected]> Date: Fri, 21 Sep 2012 11:16:28 -0400 Subject: support out-of-source build - +Forwarded: https://github.com/pezmaster31/bamtools/pull/117 --- CMakeLists.txt | 5 +++-- src/ExportHeader.cmake | 2 +- diff --git a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch index 1a35403..ddd0575 100644 --- a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch +++ b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch @@ -3,7 +3,7 @@ Date: Wed, 7 Nov 2012 19:11:51 -0700 Subject: Install libbamtools to /usr/lib. Installing libraries to /usr/lib/bamtools requires setting LD_LIBRARY_PATH or the executable's rpath. Installing libraries to /usr/lib is cleaner. - +Forwarded: https://github.com/pezmaster31/bamtools/pull/82 --- src/api/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/patches/0006-Fix-Doxyfile-input-source-path.patch b/debian/patches/0006-Fix-Doxyfile-input-source-path.patch index b4cc12d..43ebfbd 100644 --- a/debian/patches/0006-Fix-Doxyfile-input-source-path.patch +++ b/debian/patches/0006-Fix-Doxyfile-input-source-path.patch @@ -1,7 +1,7 @@ From: Kevin Murray <[email protected]> Date: Thu, 24 Sep 2015 18:04:10 +1000 Subject: Fix Doxyfile input source path - +Forwarded: https://github.com/pezmaster31/bamtools/pull/118 --- docs/Doxyfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/patches/0007-Big_Endian.patch b/debian/patches/0007-Big_Endian.patch index e9235d4..efc75ad 100644 --- a/debian/patches/0007-Big_Endian.patch +++ b/debian/patches/0007-Big_Endian.patch @@ -1,7 +1,7 @@ -Description: read bam files on big endian systems +Subject: read bam files on big endian systems Author: Dominique Belhachemi <[email protected]> Bug-Debian: https://bugs.debian.org/807979 -Forwarded: https://github.com/pezmaster31/bamtools/issues/113 +Forwarded: https://github.com/pezmaster31/bamtools/pull/119 Index: bamtools/src/api/BamAux.h =================================================================== diff --git a/debian/patches/doxygen-tweak b/debian/patches/doxygen-tweak new file mode 100644 index 0000000..400ab28 --- /dev/null +++ b/debian/patches/doxygen-tweak @@ -0,0 +1,66 @@ +From: Michael R. Crusoe <[email protected]> +Subject: fixes a couple Doxygen warnings +Forwarded: https://github.com/pezmaster31/bamtools/pull/120 + +--- bamtools.orig/src/api/BamMultiReader.cpp ++++ bamtools/src/api/BamMultiReader.cpp +@@ -361,10 +361,10 @@ + method can be useful when you know, for example, that your BAM files are sorted + by coordinate but upstream processes did not set the header tag properly. + +- \note This method should \bold not be called while reading alignments via ++ \note This method should \b not be called while reading alignments via + GetNextAlignment() or GetNextAlignmentCore(). For proper results, you should + call this method before (or immediately after) opening files, rewinding, +- jumping, etc. but \bold not once alignment fetching has started. There is ++ jumping, etc. but \b not once alignment fetching has started. There is + nothing in the API to prevent you from doing so, but the results may be + unexpected. + +--- bamtools.orig/docs/Doxyfile ++++ bamtools/docs/Doxyfile +@@ -1454,7 +1454,7 @@ + # DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory + # containing the font. + +-DOT_FONTNAME = FreeSans ++# DOT_FONTNAME = FreeSans + + # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. + # The default size is 10pt. +--- bamtools.orig/src/api/BamAlignment.h ++++ bamtools/src/api/BamAlignment.h +@@ -143,12 +143,13 @@ + bool SkipToNextTag(const char storageType, + char*& pTagData, + unsigned int& numBytesParsed) const; +- ++ //! \internal + // internal data + private: + + struct BamAlignmentSupportData { +- ++ ++ //! \internal + // data members + std::string AllCharData; + uint32_t BlockLength; +@@ -156,7 +157,8 @@ + uint32_t QueryNameLength; + uint32_t QuerySequenceLength; + bool HasCoreOnly; +- ++ ++ //! \internal + // constructor + BamAlignmentSupportData(void) + : BlockLength(0) +@@ -171,7 +173,6 @@ + friend class Internal::BamWriterPrivate; + + mutable std::string ErrorString; // mutable to allow updates even in logically const methods +- //! \endinternal + }; + + // --------------------------------------------------------- diff --git a/debian/patches/gcc-6_compat b/debian/patches/gcc-6_compat new file mode 100644 index 0000000..f1a168d --- /dev/null +++ b/debian/patches/gcc-6_compat @@ -0,0 +1,20 @@ +From d5c951f45ed768570df65e29ba9ab9eef2369f37 Mon Sep 17 00:00:00 2001 +From: Matei David <[email protected]> +Date: Wed, 3 Feb 2016 23:50:26 -0500 +Subject: [PATCH] add c++98 compile and link flag +Forwarded: https://github.com/pezmaster31/bamtools/pull/116 + +--- + CMakeLists.txt | 1 + + 1 file changed, 1 insertion(+) + +--- bamtools.orig/CMakeLists.txt ++++ bamtools/CMakeLists.txt +@@ -42,6 +42,7 @@ + + # define compiler flags for all code + set( CMAKE_BUILD_TYPE Release ) ++set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" ) + add_definitions( -Wall -D_FILE_OFFSET_BITS=64 ) + + # ----------------------------------------------- diff --git a/debian/patches/non-deprecated-jsoncpp-function-names b/debian/patches/non-deprecated-jsoncpp-function-names new file mode 100644 index 0000000..7b9b73f --- /dev/null +++ b/debian/patches/non-deprecated-jsoncpp-function-names @@ -0,0 +1,15 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Use the non-deprecated function name +Forwarded: https://github.com/pezmaster31/bamtools/pull/121 + +--- bamtools.orig/src/toolkit/bamtools_filter.cpp ++++ bamtools/src/toolkit/bamtools_filter.cpp +@@ -647,7 +647,7 @@ + if ( !reader.parse(document, root) ) { + // use built-in error reporting mechanism to alert user what was wrong with the script + cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl +- << reader.getFormatedErrorMessages(); ++ << reader.getFormattedErrorMessages(); + return false; + } + diff --git a/debian/patches/series b/debian/patches/series index 8e3563c..d399e0c 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,6 @@ +doxygen-tweak 0001-ignore-thirdparty-and-fix-jsoncpp.patch +non-deprecated-jsoncpp-function-names 0002-support-out-of-source-build.patch 0003-remove-custom-ExportHeader-function-use-install-inst.patch 0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch @@ -6,3 +8,5 @@ 0006-Fix-Doxyfile-input-source-path.patch 0007-Big_Endian.patch 0008_Cmake_Test.patch +spelling +gcc-6_compat diff --git a/debian/patches/spelling b/debian/patches/spelling new file mode 100644 index 0000000..a77f66a --- /dev/null +++ b/debian/patches/spelling @@ -0,0 +1,15 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Fix typo +Forwarded: https://github.com/pezmaster31/bamtools/pull/122 + +--- bamtools.orig/src/toolkit/bamtools_split.cpp ++++ bamtools/src/toolkit/bamtools_split.cpp +@@ -199,7 +199,7 @@ + + // if we get here, no property was specified + cerr << "bamtools split ERROR: no property given to split on... " << endl +- << "Please use -mapped, -paired, -reference, or -tag TAG to specifiy desired split behavior." << endl; ++ << "Please use -mapped, -paired, -reference, or -tag TAG to specify desired split behavior." << endl; + return false; + } + diff --git a/debian/rules b/debian/rules index 5216d3d..bf8fdfa 100755 --- a/debian/rules +++ b/debian/rules @@ -9,24 +9,31 @@ DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') %: dh $@ --parallel -override_dh_auto_build: - dh_auto_build +override_dh_auto_configure-indep: + +override_dh_auto_test-indep: + +override_dh_auto_build-indep: + doxygen -u docs/Doxyfile doxygen docs/Doxyfile + mv docs/Doxyfile.bak docs/Doxyfile -override_dh_install: +override_dh_install-indep: + dh_install --indep + rm -f debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js + ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js + +override_dh_install-arch: d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ debian/tmp/usr/lib/lib*.so - dh_install + dh_install --arch # no need to install different versions of bamtools rm -rf debian/$(DEBPKGNAME)/usr/bin/$(DEBPKGNAME) mv debian/$(DEBPKGNAME)/usr/bin/$(DEBPKGNAME)-[0-9]* debian/$(DEBPKGNAME)/usr/bin/$(DEBPKGNAME) - rm -f debian/libbamtools-dev/usr/share/doc/libbamtools-dev/html/jquery.js - ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-dev/usr/share/doc/libbamtools-dev/html/jquery.js - #override_dh_installman: # LD_LIBRARY_PATH=debian/tmp/usr/lib:${LD_LIBRARY_PATH} help2man --name "a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files" --no-info --no-discard-stderr debian/tmp/usr/bin/bamtools > debian/bamtools.1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bamtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
